{"entity":{"id":"star-salmon","kind":"term","name":"STAR and Salmon (RNA-seq alignment and quantification)","aka":["STAR aligner","STAR RNA-seq aligner","Salmon quantification","Salmon quantifier","pseudoalignment"],"tldr":"STAR lines sequencing reads up against the genome and Salmon estimates how much of each transcript is present; they are the two most common first steps of an RNA-seq pipeline.","summary":"STAR (Spliced Transcripts Alignment to a Reference) is the ultrafast universal RNA-seq aligner described by Dobin and colleagues and used by the GDC pipeline; Salmon, from Patro and colleagues, quantifies transcript expression quickly and with correction for sequence and GC bias, using a lightweight mapping rather than full alignment. Which tool, genome build and annotation were used are provenance fields a model's training data should record, because they change the numbers.","asOf":"2026-09-24","links":[{"label":"STAR on GitHub (alexdobin/STAR)","url":"https://github.com/alexdobin/STAR"},{"label":"Dobin et al., STAR: ultrafast universal RNA-seq aligner (Bioinformatics 2013)","url":"https://doi.org/10.1093/bioinformatics/bts635"},{"label":"Salmon documentation","url":"https://salmon.readthedocs.io/en/latest/"},{"label":"Patro et al., Salmon (Nature Methods 2017)","url":"https://doi.org/10.1038/nmeth.4197"}],"tags":["cansim-terms"],"related":["ngs-bioinformatics-software","cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["bulk-rna-seq","tpm-fpkm-counts","genome-builds"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/star-salmon."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Genomics & genetics"},"route":"/terms/star-salmon/","neighbours":{"technology":[{"id":"ngs-bioinformatics-software","kind":"technology","name":"Clinical NGS bioinformatics and variant interpretation","route":"/technologies/ngs-bioinformatics-software/"}],"term":[{"id":"bulk-rna-seq","kind":"term","name":"Bulk RNA sequencing (RNA-seq) and the full transcriptome","route":"/terms/bulk-rna-seq/"},{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"genome-builds","kind":"term","name":"Genome builds: GRCh38 versus hg19 (GRCh37)","route":"/terms/genome-builds/"},{"id":"tpm-fpkm-counts","kind":"term","name":"TPM, FPKM and raw counts (expression units)","route":"/terms/tpm-fpkm-counts/"}]}}